diff options
| -rwxr-xr-x | genenetwork-local-container.sh | 316 |
1 files changed, 159 insertions, 157 deletions
diff --git a/genenetwork-local-container.sh b/genenetwork-local-container.sh index 5cf4655..0f873a7 100755 --- a/genenetwork-local-container.sh +++ b/genenetwork-local-container.sh @@ -79,180 +79,182 @@ if [ -z "${HOME:-}" ]; then exit 1 fi -log "INFO" "Creating system directories..." -for dir in "${SYSTEM_DIRECTORIES[@]}"; do - # Check if directory exists and is accessible - if [ -d "$dir" ]; then - if [ -w "$dir" ]; then - log "DEBUG" "Directory exists and is writable: $dir" - else - log "WARNING" "Directory exists but is not writable: $dir. Making this writable" - sudo chown -R "$USER" "$dir" - fi - continue - fi +if [ "$1" = "--init-container" ]; then + log "INFO" "Creating system directories..." + for dir in "${SYSTEM_DIRECTORIES[@]}"; do + # Check if directory exists and is accessible + if [ -d "$dir" ]; then + if [ -w "$dir" ]; then + log "DEBUG" "Directory exists and is writable: $dir" + else + log "WARNING" "Directory exists but is not writable: $dir. Making this writable" + sudo chown -R "$USER" "$dir" + fi + continue + fi - # Attempt to create directory - log "INFO" "Creating directory: $dir" - if [ -w "$(dirname "$dir")" ]; then - # Parent directory is writable, try without sudo - if ! mkdir -p "$dir"; then - log "ERROR" "Failed to create directory without sudo: $dir" - exit 1 - fi - else - # Parent directory requires root, use sudo - if ! sudo mkdir -p "$dir"; then - log "ERROR" "Failed to create directory with sudo: $dir" - exit 1 - fi - # Set ownership to current user if created with sudo - if ! sudo chown "$USER:$USER" "$dir"; then - log "WARNING" "Failed to set ownership for: $dir" - fi - fi -done - -# Check and copy configuration files -log "INFO" "Checking and copying configuration files..." -for src in "${!FILE_MAPPINGS[@]}"; do - dest="${FILE_MAPPINGS[$src]}" - log "INFO" "Processing $src -> $dest" + # Attempt to create directory + log "INFO" "Creating directory: $dir" + if [ -w "$(dirname "$dir")" ]; then + # Parent directory is writable, try without sudo + if ! mkdir -p "$dir"; then + log "ERROR" "Failed to create directory without sudo: $dir" + exit 1 + fi + else + # Parent directory requires root, use sudo + if ! sudo mkdir -p "$dir"; then + log "ERROR" "Failed to create directory with sudo: $dir" + exit 1 + fi + # Set ownership to current user if created with sudo + if ! sudo chown "$USER:$USER" "$dir"; then + log "WARNING" "Failed to set ownership for: $dir" + fi + fi + done - # Check if source file exists - if [ ! -f "$src" ]; then - log "ERROR" "Source file does not exist: $src" - exit 1 - fi + # Check and copy configuration files + log "INFO" "Checking and copying configuration files..." + for src in "${!FILE_MAPPINGS[@]}"; do + dest="${FILE_MAPPINGS[$src]}" + log "INFO" "Processing $src -> $dest" - # Check if destination file exists - if [ ! -f "$dest" ]; then - log "INFO" "Destination file does not exist, copying $src to $dest" - mkdir -p "$(dirname "$dest")" - if ! cp "$src" "$dest"; then - log "ERROR" "Failed to copy $src to $dest" + # Check if source file exists + if [ ! -f "$src" ]; then + log "ERROR" "Source file does not exist: $src" exit 1 - fi - continue - fi + fi - # Compare files using diff - log "INFO" "Comparing $src with $dest" - if diff_output=$(diff -u "$dest" "$src" 2>&1); then - log "INFO" "Files $src and $dest are identical" - else - log "INFO" "Differences found between $src and $dest:" - echo "$diff_output" >&2 - log "INFO" "Copying $src to $dest" - if ! cp "$src" "$dest"; then - log "ERROR" "Failed to copy $src to $dest" - exit 1 - fi - fi -done + # Check if destination file exists + if [ ! -f "$dest" ]; then + log "INFO" "Destination file does not exist, copying $src to $dest" + mkdir -p "$(dirname "$dest")" + if ! cp "$src" "$dest"; then + log "ERROR" "Failed to copy $src to $dest" + exit 1 + fi + continue + fi + + # Compare files using diff + log "INFO" "Comparing $src with $dest" + if diff_output=$(diff -u "$dest" "$src" 2>&1); then + log "INFO" "Files $src and $dest are identical" + else + log "INFO" "Differences found between $src and $dest:" + echo "$diff_output" >&2 + log "INFO" "Copying $src to $dest" + if ! cp "$src" "$dest"; then + log "ERROR" "Failed to copy $src to $dest" + exit 1 + fi + fi + done -is_git_repository() { - local dir="$1" - # Check for standard repository - if [ -d "$dir/.git" ]; then - if [ -f "$dir/.git/HEAD" ] && [ -d "$dir/.git/refs" ]; then - log "DEBUG" "Detected standard Git repository: $dir" + is_git_repository() { + local dir="$1" + # Check for standard repository + if [ -d "$dir/.git" ]; then + if [ -f "$dir/.git/HEAD" ] && [ -d "$dir/.git/refs" ]; then + log "DEBUG" "Detected standard Git repository: $dir" + return 0 + else + log "ERROR" "Directory $dir/.git exists but is not a valid Git repository" + return 1 + fi + # Check for bare repository + elif [ -f "$dir/HEAD" ] && [ -d "$dir/refs" ] && [ -d "$dir/objects" ]; then + log "DEBUG" "Detected bare Git repository: $dir" return 0 - else - log "ERROR" "Directory $dir/.git exists but is not a valid Git repository" + else + log "ERROR" "$dir exists but is not a Git repository (neither standard nor bare)" return 1 - fi - # Check for bare repository - elif [ -f "$dir/HEAD" ] && [ -d "$dir/refs" ] && [ -d "$dir/objects" ]; then - log "DEBUG" "Detected bare Git repository: $dir" - return 0 - else - log "ERROR" "$dir exists but is not a Git repository (neither standard nor bare)" - return 1 - fi -} -# Clone GeneNetwork projects -log "INFO" "Cloning GeneNetwork projects..." -for project_entry in "${GN_PROJECTS[@]}"; do - IFS=':' read -r project repo_url <<< "$project_entry" - dir="$BASE_DIR/$project" - if [ ! -d "$dir" ]; then - log "INFO" "Cloning $project from $repo_url to $dir" - if ! git clone "$repo_url" "$dir"; then - log "ERROR" "Failed to clone $project" + fi + } + # Clone GeneNetwork projects + log "INFO" "Cloning GeneNetwork projects..." + for project_entry in "${GN_PROJECTS[@]}"; do + IFS=':' read -r project repo_url <<< "$project_entry" + dir="$BASE_DIR/$project" + if [ ! -d "$dir" ]; then + log "INFO" "Cloning $project from $repo_url to $dir" + if ! git clone "$repo_url" "$dir"; then + log "ERROR" "Failed to clone $project" + exit 1 + fi + else + log "DEBUG" "Directory exists, skipping clone: $dir" + if ! is_git_repository "$dir"; then + log "ERROR" "$dir exists but is not a Git repository" + exit 1 + fi + fi + done + + FLASK_SESSION="$BASE_DIR/genenetwork2/flask_session" + log "INFO" "Checking FLASK_SESSION directory: $FLASK_SESSION" + if [ ! -d "$FLASK_SESSION" ]; then + log "INFO" "Creating FLASK_SESSION directory: $FLASK_SESSION" + if ! mkdir -p "$FLASK_SESSION"; then + log "ERROR" "Failed to create FLASK_SESSION directory: $FLASK_SESSION" exit 1 - fi + fi else - log "DEBUG" "Directory exists, skipping clone: $dir" - if ! is_git_repository "$dir"; then - log "ERROR" "$dir exists but is not a Git repository" - exit 1 - fi + log "DEBUG" "FLASK_SESSION directory already exists: $FLASK_SESSION" fi -done -FLASK_SESSION="$BASE_DIR/genenetwork2/flask_session" -log "INFO" "Checking FLASK_SESSION directory: $FLASK_SESSION" -if [ ! -d "$FLASK_SESSION" ]; then - log "INFO" "Creating FLASK_SESSION directory: $FLASK_SESSION" - if ! mkdir -p "$FLASK_SESSION"; then - log "ERROR" "Failed to create FLASK_SESSION directory: $FLASK_SESSION" - exit 1 + + # Verify container SCM file exists + if [ ! -f "$CONTAINER_SCM" ]; then + log "ERROR" "Container SCM file not found: $CONTAINER_SCM" + exit 1 fi -else - log "DEBUG" "FLASK_SESSION directory already exists: $FLASK_SESSION" -fi + # Create Guix system container + log "INFO" "Creating Guix system container..." + SHARE_OPTS=( + "--share=$BASE_DIR/var/log=/var/log" + "--share=$BASE_DIR/var/genenetwork=/var/genenetwork" + "--share=$BASE_DIR/etc/genenetwork/conf=/etc/genenetwork/conf" + "--share=$BASE_DIR/etc/genenetwork=/etc/genenetwork" + "--share=$BASE_DIR/var/lib/redis=/var/lib/redis" + "--share=$BASE_DIR/var/lib/virtuoso=/var/lib/virtuoso" + "--share=$BASE_DIR/genenetwork2=/genenetwork2" + "--share=$BASE_DIR/genenetwork3=/genenetwork3" + "--share=$BASE_DIR/gn-auth=/gn-auth" + "--share=$BASE_DIR/var/lib/xapian=/var/lib/xapian" + "--share=$BASE_DIR/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite" + "--share=$BASE_DIR/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa" + "--share=/tmp/local-container=/tmp" + "--share=$BASE_DIR/gn-docs=/var/lib/gn-docs" + "--share=/run/mysqld=/run/mysqld" + ) -# Verify container SCM file exists -if [ ! -f "$CONTAINER_SCM" ]; then - log "ERROR" "Container SCM file not found: $CONTAINER_SCM" - exit 1 -fi + container_script=$(guix system container \ + --network \ + --load-path=. \ + --verbosity=3 \ + "${SHARE_OPTS[@]}" \ + "$CONTAINER_SCM") -# Create Guix system container -log "INFO" "Creating Guix system container..." -SHARE_OPTS=( - "--share=$BASE_DIR/var/log=/var/log" - "--share=$BASE_DIR/var/genenetwork=/var/genenetwork" - "--share=$BASE_DIR/etc/genenetwork/conf=/etc/genenetwork/conf" - "--share=$BASE_DIR/etc/genenetwork=/etc/genenetwork" - "--share=$BASE_DIR/var/lib/redis=/var/lib/redis" - "--share=$BASE_DIR/var/lib/virtuoso=/var/lib/virtuoso" - "--share=$BASE_DIR/genenetwork2=/genenetwork2" - "--share=$BASE_DIR/genenetwork3=/genenetwork3" - "--share=$BASE_DIR/gn-auth=/gn-auth" - "--share=$BASE_DIR/var/lib/xapian=/var/lib/xapian" - "--share=$BASE_DIR/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite" - "--share=$BASE_DIR/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa" - "--share=/tmp/local-container=/tmp" - "--share=$BASE_DIR/gn-docs=/var/lib/gn-docs" - "--share=/run/mysqld=/run/mysqld" -) - -container_script=$(guix system container \ - --network \ - --load-path=. \ - --verbosity=3 \ - "${SHARE_OPTS[@]}" \ - "$CONTAINER_SCM") + log $container_script -log $container_script + # Create symbolic links + log "INFO" "Creating symbolic links..." + if ! sudo ln -sf "$container_script" "$CONTAINER_BIN"; then + log "ERROR" "Failed to create symbolic link: $CONTAINER_BIN" + exit 1 + fi -# Create symbolic links -log "INFO" "Creating symbolic links..." -if ! sudo ln -sf "$container_script" "$CONTAINER_BIN"; then - log "ERROR" "Failed to create symbolic link: $CONTAINER_BIN" - exit 1 -fi + if ! sudo ln -sf "$container_script" "$GC_ROOT"; then + log "ERROR" "Failed to create GC root link: $GC_ROOT" + exit 1 + fi -if ! sudo ln -sf "$container_script" "$GC_ROOT"; then - log "ERROR" "Failed to create GC root link: $GC_ROOT" - exit 1 + log "INFO" "Setup completed successfully!" + log "INFO" "Container script: $container_script" + log "INFO" "Run with: $CONTAINER_BIN" + log "INFO" "Email: test@development.user" + log "INFO" "Password: testpasswd" fi - -log "INFO" "Setup completed successfully!" -log "INFO" "Container script: $container_script" -log "INFO" "Run with: $CONTAINER_BIN" -log "INFO" "Email: test@development.user" -log "INFO" "Password: testpasswd" |